As storm cleanup commences, some e-commerce sites are still down.

The storm that hit the East Coast on Monday knocked out Ann Taylor’s web site, according to a post on the clothing retailer’s Facebook page. This morning, Ann Taylor, operated by Ann Inc., No 92 in the Internet Retailer Top 500 Guide, posted an update reading: “Our site is still down for maintenance, as we were seriously impacted by Hurricane Sandy. We are working to get it back up and running as quickly as possible, and will keep you updated as the situation progresses.” At 2 p.m. Eastern time, the site was still down and sporting a banner linking to a list of Ann Taylor store locations across the country.

The retailer is not alone in still dealing with the aftermath of Hurricane Sandy. Earlier this morning, eyewear seller Warby Parker noted on its homepage that its offices would be closed until 1 p.m. Eastern Time because of Sandy, with no one to answer phones or e-mails. The message also assured customers they need not worry about returning their try-on glasses by mail while UPS was still having troubles with shipping delays. This afternoon the site appeared up and running as normal.

Meanwhile, 1-800-Flowers.com Inc., which experienced problems earlier in the week, sent an e-mail to customers saying the staff’s thoughts were with those affected by the storm. “Here at 1800Flowers.com, we are situated in an area that was severely impacted by the storm,” the message reads. “Having experienced some of the storm’s worst damage firsthand, every one of us knows what many of you are going through.” The site still displays an unusual domain, ww31, in its address today.

Even sites that are operational have issues with shipping and staff, especially those in the New York metropolitan area.

Kevin Ryan, founder and CEO of flash sales retailer Gilt Group, No. 49 in the Top 500, says his e-commerce site has no problems, but its main office in Manhattan is still closed and will likely be tomorrow as well. So, some employees are setting up a temporary office in Brooklyn for staff that still lack power and can’t work from home, while others are working from Ryan’s home on the Upper West Side of Manhattan, he says. Fortunately Gilt’s customer service centers are in Oregon and Ireland, he says, and most of its warehouses are in Kentucky, with none in the New York area.

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His main concern was that Gilt would be delayed in its ability to shoot new product photos, since the studio is in the Manhattan office, he says. However, today he learned that the studio can open tomorrow; Gilt was able to make do in the meantime, as it shoots photos three to five days in advance, he says, but the delay would have been a problem if it lasted longer.

The retailer did feel Sandy’s impact on sales slightly, Ryan says, estimating that revenue is down about 10% to 20% so far this week. But he’s not concerned, especially given the upcoming holidays—consumers will still need to buy the same number of gifts in the end, he says.

Shipping times for Gilt may slow slightly, Ryan adds, since some UPS planes were unable to get out of New York until the first area airports opened today. According to a spokesman for FedEx Corp., which also had to stop flying in the Northeast earlier this week, it was able to land a first plane this morning when Newark Liberty International Airport opened at 7 a.m. Eastern, he says, and John F. Kennedy International Airport announced it expected to re-open after noon.

All FedEx services will be back to normal once the New York public transit system is fully functioning and staff can get to work, the spokesman adds, though it doesn’t expect too many hiccups until then. The parcel carrier employs 14 meteorologists who advised it during the week and a half it spent preparing to divert shipping routes for the storm, he says, including switching from planes to trucks for many deliveries in the Northeast earlier this week.

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FedEx, UPS and the United States Postal Service are all posting updated information about service and shipping delays on their web sites.

“Some areas affected by Sandy, specifically in the Northeast, are experiencing some service disruptions,” says a USPS spokeswoman. “We have emergency operation plans in place to expedite recovery efforts, including making sure there is timely delivery of mailed ballots. We are continuing to monitor the situation and will make adjustments to our delivery operations as necessary.”

On Tuesday, Amazon.com Inc., No. 1 in the Top 500, told merchants that use its warehouses and shipping services in the Fulfillment by Amazon program to expect delays, the retailer says. It also asked marketplace sellers to temporarily deactivate listings for items they would not be able to ship in the usual amount of time, Amazon confirms.

Order processing and fulfillment vendor Innotrac Corp. has strategically placed its warehouses inland and on high ground in order to avoid weather-related problems, the company says, which worked out well during Sandy. It hasn’t had any problems fulfilling orders for clients this week, it says. One retailer in Innotrac’s SmartHub benchmarking study that did experience delays is offering customers a $30 credit on their next order to make up for the inconvenience, the company says, declining to reveal the retailer’s name. “It’s a higher-end brand, so it would definitely make sense for their clientele,” an Innotrac spokeswoman says.

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Meanwhile some retailers are adorning e-mail subject lines with Sandy-related lingo, according to The Retail Email Blog, written by Chad White, research director of e-mail service provider Responsys Inc., who tracks retailers’ e-mail marketing campaigns. Among them are Kmart, which Monday sent out messages with the subject line “Storm season’s here: Kmart has what you need‏,” and Wal-Mart Stores Inc., No. 4 in the Top 500, which yesterday sent “It’s raining apparel savings. Plus everyday low prices on cold weather essentials.” American Apparel however, sparked some negative social chatter for a sale directed at consumers in states affected by Sandy that offered 20% off everything for 36 hours “in case you’re bored during the storm,” the blog and other news outlets report.

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